Question: extract some feature from peak?
gravatar for star
11 weeks ago by
star140 wrote:

I did peak calling using MACS2. Now I like to calculate some features (like below) from them but I am not sure which tools can be helpful.

  • peak height
  • number of read / count for each peak -- > I think map / genomecoverage function of bedtools may be helpful but I am not sure!

Thanks for your help in advanced.

ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by star140

you may use some tools in bedtools suite- intersecting the bam with the intervals bed file by intersectBed, use coverage to compute depth and breadth, and even genomecov and an in house script.

ADD REPLYlink written 11 weeks ago by biobiu90
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